Data from: Inbreeding effects on gene-specific DNA methylation among tissues of Chinook salmon

Inbreeding depression is the loss of fitness resulting from the mating of genetically-related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, though recent research has identified DNA methylation as also having a role in inbreeding effects. Since inbreeding depression and DNA methylation change with age and environmental stress, DNA methylation is a likely candidate for the regulation of genes associated with inbreeding depression. Here we use a targeted, multi-gene approach to assess methylation at 22 growth, metabolic, immune, and stress-related genes. We developed PCR-based DNA methylation assays to test the effects of intense inbreeding on intragenic gene-specific methylation in inbred and outbred Chinook salmon. Inbred fish had altered methylation at three genes, CK-1, GTIIBS, and hsp70, suggesting that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole-genome effects. While we did not find a significant inbreeding by age interaction, we found that DNA methylation generally increases with age, though methylation decreased with age in five genes, CK-1, IFNɣ, HNRNP, hsc71, and FSHb, potentially due to environmental context and sexual maturation. As expected, we found methylation patterns differed among tissue types, highlighting the need for careful selection of target tissue for methylation studies. This study provides insight into the role of epigenetic effects on aging, environment and tissue function in Chinook salmon and shows that methylation is a targeted and regulated cellular process. We provide the first evidence of epigenetically-based inbreeding depression in vertebrates.近交衰退（inbreeding depression）指的是亲缘个体间交配所导致的适合度下降。传统上，近交衰退的研究多聚焦于遗传效应，尽管近期研究已证实DNA甲基化（DNA methylation）同样参与近交效应的调控。鉴于近交衰退与DNA甲基化均会随年龄增长及环境胁迫发生动态变化，DNA甲基化极有可能是调控近交衰退相关基因的关键表观遗传机制。本研究采用靶向多基因研究策略，对22个与生长、代谢、免疫及胁迫响应相关的基因的甲基化水平进行检测。我们建立了基于聚合酶链式反应（PCR）的DNA甲基化检测体系，以探究高强度近交对近交组与远交组奇努克鲑（Chinook salmon）基因内特异性甲基化的影响。近交个体在CK-1、GTIIBS及hsp70三个基因位点的甲基化水平出现显著改变，这表明与近交衰退相关的甲基化变化具有基因靶向性，并非全基因组层面的广谱效应。尽管未检测到近交与年龄间的显著交互效应，但我们观察到DNA甲基化整体呈现随年龄升高的趋势，不过CK-1、IFNɣ、HNRNP、hsc71及FSHb这5个基因的甲基化水平却随年龄降低，这一现象可能与环境背景及个体性成熟过程相关。正如预期，不同组织类型的甲基化模式存在显著差异，这凸显了甲基化研究中谨慎选择靶组织的重要性。本研究揭示了表观遗传效应在奇努克鲑衰老、环境适应及组织功能调控中的作用，并证实甲基化是一种受精准调控的靶向细胞过程。本研究首次在脊椎动物中提供了基于表观遗传机制的近交衰退的实验证据。